The emerging applications of nanotechnology in the discipline of healthcare include development of a diversity of formulations from traditional dosage forms to targeted drug-delivery systems and even beyond. Synthesis, processing, and characterization of their micromeritics, as well as the methods of nanoparticularization and their physicochemical stabilization at the prototype level, have been quite successful, though such nanosystems possess umpteen challenges at subsequent stages of scale-up. Often this has led to the breakdown of such pharmaceutical systems, resulting in compromised stability (physical and/or chemical), with differing levels of predictability in anticipating their biopharmaceutical and potential clinical outcomes. Hence, a more organized approach for understanding the essential requirements to develop nanotechnology-based pharmaceutical systems is required that are robust and can withstand the rigors of various stages of drug development. The present chapter, in this regard, not only provides insight into the practical application of nanotechnology for augmenting therapeutic performance of biopharmaceutical agents, but also focuses on the vital challenges and opportunities for evaluating the biopharmaceutical applications of nanoparticulate systems towards meaningful clinical outcomes, including pivotal considerations regarding their scale-up from laboratory to clinic. Besides the experiential inputs, some important case studies on nanostructured formulations of various documented therapeutic agents and plant-based bioactives, namely, olmesartan medoxamil, lopinavir, quercetin, and naringenin are discussed, demonstrating real-time benefits of nanotechnology tools for accomplishing the aforesaid objectives.